i had the same issue
The reason you are experiencing second gear popping is due to the shift dogs on second gear being worn and rounded off. instead of a nice clean, sharp edge for the slot the shift dog rests in and hold onto while in second gear, it is rounded off, which causes it to slide "pop" right back out when heavy throttle is applied. The reason it doesn't just go back into neutral is because as it "slides" out, it falls back and "slides" back into the next slot-hence the "popping". effect. And with every pop, it will get worse and worse. Like the other guy said, you have to take the entire motor out of the bike and split the bottom half of the engine/trans case. but dont worry, its not as bad as it seems. With parts and everything it came to about $1,200. Wanna know how to avoid having this problem in the future? first of all, when shiftong gears, regardless of what gear, be very gentle on the shifter. if you force the shifter into gear, it will bend the shift forks. Second, you must find that sweet spot where your R1 likes to be shifted. Believe me, it is tough. i am still searching for mine. i have found it best to shift early on in the lower engine RPM's.
If you have any further questions, just ask. I am pretty knowledgable now. Wish i weren't tho.
Last edited by dandable; 08-15-2008 at 02:28 PM.